+Open data
-Basic information
Entry | Database: PDB / ID: 5iwj | |||||||||||||||||||||||||||||||
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Title | LAmbda-[Ru(TAP)2(dppz)]2+ bound to d(CCGGGCCCGG | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Ruthenium / photooxidising / intercalation | Function / homology | : / Ru(tap)2(dppz) complex / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å | Authors | Souter, J.E. / Hall, J.P. / Cardin, C.J. | Funding support | United Kingdom, 2items |
Citation | Journal: To Be Published | Title: The binding specificity of RuTAP2dppz Authors: Souter, J.E. / Hall, J.P. / Gurung, S.P. / Brazier, J.A. / Cardin, C.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iwj.cif.gz | 19 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwj.ent.gz | 10.8 KB | Display | PDB format |
PDBx/mmJSON format | 5iwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwj ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3046.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-BA / |
#3: Chemical | ChemComp-RKL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1uL 2mM ss oligonucleotide, 1uL 3mM rac-RuTAP2dppz, 6uL of a solution containing 20mM BaCl2, 80mM KCl, 10% (V/V) hexylene glycol, 12mM spermine, 40mM Na-cacodylate pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→28 Å / Num. obs: 3455 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.88→28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.736 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.684 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→28 Å
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Refine LS restraints |
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